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首页> 外文期刊>Acta Physiologiae Plantarum >Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq
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Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq

机译：盐胁迫下大麦叶片转录组的mRNA-Seq分析

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摘要

Salinity is a threat to crops in many parts of the world, and together with drought, it is predicted to be a serious constraint to food security. However, understanding the impact of this stressor on plants is a major challenge due to the involvementof numerous genes and regulatory pathways. While transcriptomic analyses of barley (Hordeum vulgare L.) under salt stress have been reported with microarrays, there are no reports as yet of the use of mRNA-Seq. We demonstrate the utility of mRNA-Seq by analysing cDNA libraries derived from acutely salt-stressed and unstressed leaf material of H. vulgare cv. Hindmarsh. The data yielded >50 million sequence tags which aligned to 26,944 sequences in the Unigene reference database. To gain maximum information, we performed de novo assembly of unaligned reads and discovered >3,800 contigs, termed novel tentative consensus sequences, which are either new, or significant improvements on current databases. Differential gene expression screening found 48 significantly up-regulated and 62 significantly down-regulated transcripts. The work provides comprehensive insights into genome-wide effects of salinity and is a new resource for the study of gene regulation in barley and wheat. Further, the bioinformatics workflow may be applicable to other non-model plants to establish their transcriptomes and identify unique sequences.
机译：盐分对世界许多地区的农作物构成威胁，并与干旱一起预计将严重阻碍粮食安全。然而，由于众多基因和调控途径的参与，了解这种胁迫对植物的影响是一项重大挑战。虽然已经报道了利用微阵列对大麦（大麦（Hordeum vulgare L.））在盐胁迫下的转录组学分析，但是目前尚无关于使用mRNA-Seq的报道。我们通过分析源自H. vulgare cv的急性盐胁迫和未胁迫叶片材料的cDNA文库，证明了mRNA-Seq的实用性。 Hindmarsh。数据产生了> 5000万个序列标签，与Unigene参考数据库中的26,944个序列比对。为了获得最大的信息，我们从头进行了未比对读段的重新组装，发现了3,800多个重叠群，称为新颖的暂定共有序列，它们是新的，还是对当前数据库的重大改进。差异基因表达筛选发现48个显着上调的转录本和62个显着下调的转录本。这项工作为盐度对全基因组范围的影响提供了全面的见解，是研究大麦和小麦基因调控的新资源。此外，生物信息学工作流程可适用于其他非模型植物以建立其转录组并鉴定独特序列。

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